High Throughput Genome Builds

This is a transcript of whiteboard notes from the 5/30/06 Genecats meeting.

Input Requirements

AGP File, Sequence

Output Tracks

Gap. Gold, ChromInfo, GC5

Then Repeat Masking/Window Masker and trfBig

Produces rmsk/windowMask and simpleRepeats track

Early Tracks

Genscan, Genbank Scripts, CpG Islands

Comparative Genomics

human and mouse

Candidate Genomes

(A)platypus(new + update), (A)frog update, (A)Stickleback(fish)(new + update), (A)Medaka(fish), (B)rhesus update, (B)chicken update, (A)elephant, (B)rabbit(new + update), (A)pig(new + update), (B)cat(new + update), (A)fugu update, (B)chimp update, (C)mouse, (C)human

Key: (A) = Abbreviated browser only (B) = More expanded browser (C) = Full browser

Tools

• xxxToAgp
• agpToDb builds to to RepeatMasking, include data staging ? SAN, scratch, iscratch

  verifies AGP & Sequence, sets up unmasked sequence into 500K chunks for RM, stores sequence in standard place.

• masker with or without repeat library

  Work towards windowMask automation

• Masked sequence stager
• make goldenPath downloads
• makeXxxTrack

  Work towards track by track automation

• doBlastzChainNet (how about saving run-time parameters in a metadata DB table to create README/.html information ?)

  chain/net .html file $alignSettings keyword and library function to make alignment parameter table

• Conservation (On all browsers ?)

Bugs

.html pages for tracks

QA Time

• Downloads
• Metadata, hgCentral, defaultDb, dbDb, all.joiner, READMEs
• liftOvers (between same species)
• HTML Pages
• Links and Clickthroughs

Metadata blastz parameter table

Organism	Assembly	matrix	gaps	abridged repeats	...etc...
mouse	mm8	medium	medium	yes	...etc...
human	hg19	loose	loose	no	...etc...